4YV8

Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal

4YV8 の概要

• エントリーDOI: 10.2210/pdb4yv8/pdb
• 関連するPDBエントリー: 4YVA
• 関連するBIRD辞書のPRD_ID: PRD_002162
• 分子名称: Cathepsin K, Lichostatinal, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: cathepsin k, lichostatinal, inhibitor, hydrolase-inhibitor complex, hydrolase/inhibitor
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 24311.30

構造登録者

Aguda, A.H.,Nguyen, N.T.,Bromme, D.,Brayer, G.D. (登録日: 2015-03-19, 公開日: 2016-05-04, 最終更新日: 2023-11-15)

主引用文献

Aguda, A.H.,Lavallee, V.,Cheng, P.,Bott, T.M.,Meimetis, L.G.,Law, S.,Nguyen, N.T.,Williams, D.E.,Kaleta, J.,Villanueva, I.,Davies, J.,Andersen, R.J.,Brayer, G.D.,Bromme, D.
Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.
J.Nat.Prod., 79:1962-1970, 2016

PubMed Abstract: Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

PubMed: 27498895
DOI: 10.1021/acs.jnatprod.6b00215

実験手法

X-RAY DIFFRACTION (2 Å)